Re: [Spglib-users] symmetrizing positions/cell vectors without altering cell?

[Atsushi T. <atz...@gm...>]

Good!

Togo

On Mon, Sep 25, 2017 at 10:49 PM, Noam Bernstein
<noa...@nr...> wrote:
> On Sep 25, 2017, at 9:15 AM, Atsushi Togo <atz...@gm...> wrote:
>
> If the distortion is not that much, then the approach by
> Grosse-Kunstleve and Adams should work. If you write a python script,
> I think I can comment to it. The C-code is about here,
> https://github.com/atztogo/spglib/blob/master/src/site_symmetry.c#L244
>
>
>
> Hmm.  I tried something like this initially, and it wasn't working at all,
> but I must have had a bug, since I redid it cleanly (so I could show the
> code), and the new version's apparently working.  Maybe because I was coding
> for an audience I was more careful.  In any case, while I think it would be
> useful to have a version of standardize_cell() that only moved atoms,
> without touching the cell vectors, I think my problem is solved for now
> (especially if I can recode it without a tight loop in python).  It should
> probably be redone without so many tight loops in explicit python, but here
> it is, in case it’s useful for anyone else:
>
> #!/usr/bin/env python
>
> import os, sys
> import spglib, ase, ase.io
> import numpy as np
>
> at = ase.io.read(sys.argv[1])
>
> dataset = spglib.get_symmetry_dataset(at, symprec=1.0e-5)
> sys.stderr.write("precise initial symmetry group number {}, international
> (Hermann-Mauguin) {} Hall {} prec
> {}\n".format(dataset["number"],dataset["international"],dataset["hall"],1.0e-5))
> dataset = spglib.get_symmetry_dataset(at, symprec=0.1)
> sys.stderr.write("loose initial symmetry group number {}, international
> (Hermann-Mauguin) {} Hall {} prec
> {}\n".format(dataset["number"],dataset["international"],dataset["hall"],0.1))
>
> p = at.get_scaled_positions()
> cell = at.get_cell()
>
> new_position = np.zeros(at.get_positions().shape)
> for i in range(len(at)):
>     # zero accumulators for rot and transl
>     mean_r = np.zeros((3,3))
>     mean_t = np.zeros((3))
>     n_contrib=0
>     position = p[i][:]
>     # loop over opreations
>     for (r, t) in zip(dataset['rotations'], dataset['translations']):
>         # transformed position
>         pos = np.dot(r, position) + t
>         # if it's close to periodic image, contribute to accumulators
>         dp = pos - position
>         dp_in_cell = dp - np.round(dp)
>         if np.linalg.norm(dp_in_cell) < 0.1:
>             mean_r += r
>             mean_t += t - np.round(dp)
>             n_contrib += 1
>     mean_r /= float(n_contrib)
>     mean_t /= float(n_contrib)
>
>     new_position[i,:] = np.dot(position, mean_r) + mean_t
>
> at.set_scaled_positions(new_position)
> dataset = spglib.get_symmetry_dataset(at, symprec=1.0e-5)
> sys.stderr.write("manual symmetrization got symmetry group number {},
> international (Hermann-Mauguin) {} Hall {} prec
> {}\n".format(dataset["number"],dataset["international"],dataset["hall"],1.0e-5))
> ase.io.write(sys.stdout, at, format="extxyz")
>
>
>
> thanks again,
> Noam



-- 
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...